The main advantage of using ontologies is the formalized semantics. This way a reasoner can automatically infer new statements without writing specific code.
But it's true, that you can model every Linked Data also in RDBMS and the other way around. The same is true for querying with SPARQL or SQL. You can achieve the same results. SPARQL has some advantages if your SQL query requires multiple joins. This can be expressed in a far more meaningful way in SPARQL.
The disadvantage of ontology based databases is nowadays still a lack of performance in comparison to RDBMS.